Last modified by giuliadarrigo on 2023/06/26 14:11
From version 30.1
edited by dariak
on 2022/03/22 18:07
Change comment: Migrated property [owner] from class [Collaboratory.Apps.Collab.Code.CollabClass]
To version 44.1
edited by giuliadarrigo
on 2023/06/26 14:11
Change comment: There is no comment for this version

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Title
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1 -Molecular Tools: computation of unbinding rates
1 +Molecular Tools: computation of dissociation rates
Author
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1 -XWiki.dariak
1 +XWiki.giuliadarrigo
Content
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2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -* (((
6 -= Molecular Tools: computation of unbinding rates =
5 +(((
6 += Molecular Tools: computation of dissociation rates =
7 7  )))
8 8  
9 -Authors:  D. Kokh
9 +This collab contains a set of tools and tutorials for analysing and computing unbinding rates of protein-small molecule and protein-protein complexes.
10 +
11 +Authors:  D. Kokh, G. D'Arrigo, R. Wade
10 10  )))
11 11  )))
12 12  
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16 16  (((
17 17  = What can I find here? =
18 18  
19 -Jupyter Lab workflows that helps to setup, carry out, and analyze dissociation of protein-drug and protein-protein complexes
21 +Jupyter Lab workflows that help to set up, carry out and analyze dissociation of protein-drug and protein-protein complexes.
20 20  
21 21  
22 22  (% style="text-align:center" %)
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32 32  
33 33  (% class="box" %)
34 34  (((
35 -**Computation of Protein-Protein Unbinding rates**:  Jupyter Notebooks/PP-kinetics.ipynb
37 +**Computation of Protein-Ligand Dissociation rates**: 
36 36  
37 -[[https:~~/~~/lab.ebrains.eu/user/dariak/lab/tree/drive/Shared%20with%20all/Molecular%20Tools:%20computation%20of%20%20unbinding%20rates%20>>https://lab.ebrains.eu/user/dariak/lab/tree/drive/Shared%20with%20groups/Molecular%20Tools:%20computation%20of%20%20unbinding%20rates%20]]
39 +**1st_tutorial_tauRAMD_residencetime.ipynb** to estimate residence time from pre-computed RAMD trajectories.
38 38  
41 +**2nd_tutorial_tauRAMD_egress-routes.ipynb **to investigate dissociation pathways from pre-computed RAMD trajectories.
39 39  
40 -**Computation of Protein-Ligand Unbinding rates**:  under development
43 +{{jupyterlink}}
44 +https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Molecular%20Tools%3A%20computation%20of%20dissociation%20rates%20/Training_220623/Jupyter_Notebooks
45 +{{/jupyterlink}}
46 +
47 +**Computation of Protein-Protein Dissociation rates**:
48 +
49 +under development
50 +
51 +{{jupyterlink}}
52 +https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Molecular%20Tools%3A%20computation%20of%20dissociation%20rates%20/Archive/PP-kinetics.ipynb
53 +{{/jupyterlink}}
41 41  )))
42 42  
43 43  
Collaboratory.Apps.Collab.Code.CollabClass[0]
owner
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1 +dariak